diff uniprotxml_downloader.py @ 0:0bd2688166a5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprotxml_downloader.py	Tue Mar 08 12:03:49 2016 -0500
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                         University of Minnesota
+#         Copyright 2016, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#  James E Johnson
+#
+#------------------------------------------------------------------------------
+"""
+import sys
+import re
+import optparse
+import urllib
+
+
+def __main__():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
+    parser.add_option('-r', '--reviewed', dest='reviewed', help='file path for th downloaed uniprot xml')
+    parser.add_option('-o', '--output', dest='output', help='file path for th downloaed uniprot xml')
+    parser.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False, help='Print UniProt Info')
+    parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
+    (options, args) = parser.parse_args()
+
+    taxids = options.taxon if options.taxon else ['9606']
+    taxon_queries = ['taxonomy:"%s"' % taxid for taxid in taxids]
+    taxon_query = ' OR '.join(taxon_queries)
+    if options.output:
+        dest_path = options.output
+    else:
+        dest_path = "uniprot_%s.xml" % '_'.join(taxids)
+    reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
+    url = 'http://www.uniprot.org/uniprot/?query=%s%s&force=yes&format=xml' % (taxon_query, reviewed)
+    if options.debug:
+        print >> sys.stderr, url
+    try:
+        (fname, msg) = urllib.urlretrieve(url, dest_path)
+        headers = {j[0]: j[1].strip() for j in [i.split(':', 1) for i in str(msg).strip().splitlines()]}
+        if 'Content-Length' in headers and headers['Content-Length'] == 0:
+            print >> sys.stderr, url
+            print >> sys.stderr, msg
+            exit(1)
+        elif True:
+            pass
+        else:
+            with open(dest_path, 'r') as contents:
+                while True:
+                    line = contents.readline()
+                    if options.debug:
+                        print >> sys.stderr, line
+                    if line is None or not line.startswith('<?'):
+                        break
+                    # pattern match <root or <ns:root for any ns string
+                    pattern = '^<(\w*:)?uniprot'
+                    if re.match(pattern, line):
+                        break
+                    else:
+                        print >> sys.stderr, "failed: Not a uniprot xml file"
+                        exit(1)
+
+        if options.verbose:
+            print >> sys.stdout, "NCBI Taxon ID:%s" % taxids
+            if 'X-UniProt-Release' in headers:
+                print >> sys.stdout, "UniProt-Release:%s" % headers['X-UniProt-Release']
+            if 'X-Total-Results' in headers:
+                print >> sys.stdout, "Entries:%s" % headers['X-Total-Results']
+            print >> sys.stdout, "%s" % url
+    except Exception, e:
+        print >> sys.stderr, "failed: %s" % e
+
+
+if __name__ == "__main__":
+    __main__()